The intrinsic viscosity of linear DNA

On-chip screening of SARS-CoV-2 cDNA by LAMP-integrated rotational diffusometry

The unprecedented pandemic has raised the demand for prompt, precise, and large-scale virus detection techniques to control the transmission of contagious illnesses. In this study, a loop-mediated isothermal amplification (LAMP) based on-chip platform was developed to address this challenge using rotational diffusometry and functionalized Janus particles. A recombinant plasmid containing a cDNA sequence of the SARS-CoV-2 non-structural protein 2 (nsp2) gene was employed here as a proof-of-concept for COVID-19 detection. Specifically, designed primers and the functionalized Janus particles were simultaneously loaded on a microfluidic chip to perform the LAMP reaction on a hot plate. The optimal Janus particle concentrations for diffusometric analysis were thoroughly validated, and the performance of the on-chip LAMP reaction was assessed using thermal image analysis. Utilization of the highly sensitive rotational diffusometry achieved a limit of detection of 1 pg/μL in just 10 min with a sample volume of 20 μL. Our method delivered a tenfold higher sensitivity than the conventional method by utilizing only half of its usual required time. Overall, this study proposes a potential nucleic acid (NA) amplification device to aid the rapid diagnosis of various diseases by modifying the primers for different target genes.

Type-Independent 3D Writing and Nano-Patterning of Confined Biopolymers

Biopolymers are essential building blocks that constitute cells and tissues with well-defined molecular structures and diverse biological functions. Their three-dimensional (3D) complex architectures are used to analyze, control, and mimic various cells and their ensembles. However, the free-form and high-resolution structuring of various biopolymers remain challenging because their structural and rheological control depend critically on their polymeric types at the submicron scale. Here, direct 3D writing of intact biopolymers is demonstrated using a systemic combination of nanoscale confinement, evaporation, and solidification of a biopolymer-containing solution. A femtoliter solution is confined in an ultra-shallow liquid interface between a fine-tuned nanopipette and a chosen substrate surface to achieve directional growth of biopolymer nanowires via solvent-exclusive evaporation and concurrent solution supply. The evaporation-dependent printing is biopolymer type-independent, therefore, the 3D motor-operated precise nanopipette positioning allows in situ printing of nucleic acids, polysaccharides, and proteins with submicron resolution. By controlling concentrations and molecular weights, several different biopolymers are reproducibly patterned with desired size and geometry, and their 3D architectures are biologically active in various solvents with no structural deformation. Notably, protein-based nanowire patterns exhibit pin-point localization of spatiotemporal biofunctions, including target recognition and catalytic peroxidation, indicating their application potential in organ-on-chips and micro-tissue engineering.

Molecular Dynamics Investigation of Hyaluronan in Biolubrication

Aqueous solution of strongly hydrophilic biopolymers is known to exhibit excellent lubrication properties in biological systems, such as the synovial fluid in human joints. Several mechanisms have been proposed on the biolubrication of joints, such as the boundary lubrication and the fluid exudation lubrication. In these models, mechanical properties of synovial fluid containing biopolymers are essential. To examine the role of such biopolymers in lubrication, a series of molecular dynamics simulations with an all-atom classical force field model were conducted for aqueous solutions of hyaluronan (hyaluronic acid, HA) under constant shear. After equilibrating the system, the Lees-Edwards boundary condition was imposed, with which a steady state of uniform shear flow was realized. Comparison of HA systems with hydrocarbon (pentadecane, PD) solutions of similar mass concentration indicates that the viscosity of HA solutions is slightly larger in general than that of PDs, due to the strong hydration of HA molecules. Effects of added electrolyte (NaCl) were also discussed in terms of hydration. These findings suggest the role of HA in biolubirication as a load-supporting component, with its flexible character and strong hydration structure.

Quartz crystal microbalance and atomic force microscopy to characterize mimetic systems based on supported lipids bilayer

Quartz Crystal Microbalance (QCM) with dissipation and Atomic Force Microscopy (AFM) are two characterization techniques that allow describing processes taking place at solid-liquid interfaces. Both are label-free and, when used in combination, provide kinetic, thermodynamic and structural information at the nanometer scale of events taking place at surfaces. Here we describe the basic operation principles of both techniques, addressing a non-specialized audience, and provide some examples of their use for describing biological events taking place at supported lipid bilayers (SLBs). The aim is to illustrate current strengths and limitations of the techniques and to show their potential as biophysical characterization techniques.

ZnO-loaded DNA nanogels as neutrophil extracellular trap-like structures in the treatment of mouse peritonitis

Neutrophil extracellular traps (NETs) are chromatin-based structures that are released from neutrophils during infections and prevent microbes from spreading in the body through efficient degradation of their composition. Based on this chromatin-driven strategy of capturing and killing bacteria, we designed NET-like structures using DNA and ZnO nanoparticles (NPs). DNA was first purified from kiwifruit and treated with HCl to increase hydroxyl groups in the opened-deoxylribose form. The carboxyl groups of citric acid were then thermally crosslinked with said hydroxyl and primary amine groups in DNA, forming DNA-HCl nanogels (NGs). ZnO NPs were then used as positively charged granule enzymes, adsorbed onto the DNA-HCl NG, obtaining ZnO/DNA-HCl NGs (with NET biomimicry). In an anti-inflammatory assay, ZnO/DNA-HCl NGs significantly inhibited TNF-α, IL-6, iNOS and COX-2 expression in LPS-stimulated Raw264.7 cells. Moreover, the ZnO/DNA-HCl NGs markedly alleviated clinical symptoms in LPS-induced mouse peritonitis. Finally, ZnO/DNA-HCl NGs suppressed E. coli from entering circulation in septic mice while prolonging their survival. Our results suggest that the ZnO/DNA-HCl NGs, which mimic NET-like structures in the blocking of bacteria-inducted inflammation, may be a potential therapeutic strategy for bacterial infections.

HP1 proteins compact DNA into mechanically and positionally stable phase separated domains

In mammals, HP1-mediated heterochromatin forms positionally and mechanically stable genomic domains even though the component HP1 paralogs, HP1α, HP1β, and HP1γ, display rapid on-off dynamics. Here, we investigate whether phase-separation by HP1 proteins can explain these biological observations. Using bulk and single-molecule methods, we show that, within phase-separated HP1α-DNA condensates, HP1α acts as a dynamic liquid, while compacted DNA molecules are constrained in local territories. These condensates are resistant to large forces yet can be readily dissolved by HP1β. Finally, we find that differences in each HP1 paralog's DNA compaction and phase-separation properties arise from their respective disordered regions. Our findings suggest a generalizable model for genome organization in which a pool of weakly bound proteins collectively capitalize on the polymer properties of DNA to produce self-organizing domains that are simultaneously resistant to large forces at the mesoscale and susceptible to competition at the molecular scale.

Protein intrinsic viscosity determination with the Viscosizer TD instrument: reaching beyond the initially expected applications

Intrinsic viscosity is a key hydrodynamic parameter to understand molecular structure and hydration, as well as intramolecular interactions. Commercially available instruments measure intrinsic viscosity by recording the macromolecular mobility in a capillary. These instruments monitor Taylor dispersion using an absorbance or fluorescence detector. By design, these instruments behave like U-tube viscometers. To our knowledge, there are no studies to date showing that the Viscosizer TD instrument (Malvern-Panalytical) is able to measure the intrinsic viscosity of macromolecules. In this study, we then performed our assays on the Poly(ethylene oxide) polymer (PEO), used classically as a standard for viscometry measurements and on three model proteins: the bovine serum albumin (BSA), the bevacizumab monoclonal antibody, and the RTX Repeat Domain (RD) of the adenylate cyclase toxin of Bordetella pertussis (CyaA). The presence of P20 in the samples is critical to get reliable results. The data obtained with our in-house protocol show a strong correlation with intrinsic viscosity values obtained using conventional techniques. However, with respect to them, our measurements could be performed at relatively low concentrations, between 2 and 5 mg/ml, using only 7 µL per injection. Altogether, our results show that the Viscosizer TD instrument is able to measure intrinsic viscosities in a straightforward manner. This simple and innovative approach should give a new boost to intrinsic viscosity measurements and should reignite the interest of biophysicists, immunologists, structural biologists and other researchers for this key physicochemical parameter.

Rheological Properties of DNA Molecules in Solution: Molecular Weight and Entanglement Influences

Molecular weight, stiffness, temperature, and polymer and ionic concentrations are known to widely influence the viscosity of polymer solutions. Additionally, polymer molecular weight-which is related to its dimensions in solution-is one of its most important characteristics. In this communication, low molecular weight DNA from salmon sperm was purified and then studied in solutions in a wide concentration range (between 0.5 and 1600 mg/mL). The intrinsic viscosity of this low molecular weight DNA sample was firstly determined and the evidence of the overlap concentration was detected around the concentration of 125 mg/mL. The chain characteristics of these short molecules were studied in terms of the influence of their molecular weight on the solution viscosities and on the overlap parameter CDNA[η]. Furthermore, to complete previously reported experimental data, solutions of a large molecular weight DNA from calf-thymus were studied in a high concentration range (up to 40 mg/mL). The rheological behavior is discussed in terms of the generalized master curve obtained from the variation of the specific viscosity at zero shear rate (ηsp,0) as a function of CDNA[η].

Persistent draining crossover in DNA and other semi-flexible polymers: Evidence from hydrodynamic models and extensive measurements on DNA solutions

Although the scaling theory of polymer solutions has had many successes, this type of argument is deficient when applied to hydrodynamic solution properties. Since the foundation of polymer science, it has been appreciated that measurements of polymer size from diffusivity, sedimentation, and solution viscosity reflect a convolution of effects relating to polymer geometry and the strength of the hydrodynamic interactions within the polymer coil, i.e., "draining." Specifically, when polymers are expanded either by self-excluded volume interactions or inherent chain stiffness, the hydrodynamic interactions within the coil become weaker. This means there is no general relationship between static and hydrodynamic size measurements, e.g., the radius of gyration and the hydrodynamic radius. We study this problem by examining the hydrodynamic properties of duplex DNA in solution over a wide range of molecular masses both by hydrodynamic modeling using a numerical path-integration method and by comparing with extensive experimental observations. We also considered how excluded volume interactions influence the solution properties of DNA and confirm that excluded volume interactions are rather weak in duplex DNA in solution so that the simple worm-like chain model without excluded volume gives a good leading-order description of DNA for molar masses up to 10(7) or 10(8) g/mol or contour lengths between 5 μm and 50 μm. Since draining must also depend on the detailed chain monomer structure, future work aiming to characterize polymers in solution through hydrodynamic measurements will have to more carefully consider the relation between chain molecular structure and hydrodynamic solution properties. In particular, scaling theory is inadequate for quantitative polymer characterization.

Conformation and Rheological Properties of Calf-Thymus DNA in Solution

Studies of DNA molecule behavior in aqueous solutions performed through different approaches allow assessment of the solute-solvent interactions and examination of the strong influence of conformation on its physicochemical properties, in the presence of different ionic species and ionic concentrations. Firstly, the conformational behavior of calf-thymus DNA molecules in TE buffer solution is presented as a function of temperature. Secondly, their rheological behavior is discussed, as well as the evidence of the critical concentrations, i.e., the overlap and the entanglement concentrations (C* and C_e, respectively) from steady state flow and oscillatory dynamic shear experiments. The determination of the viscosity in the Newtonian plateau obtained from flow curves η (γ˙) allows estimation of the intrinsic viscosity and the specific viscosities at zero shear when C[η] < 40. At end, a generalized master curve is obtained from the variation of the specific viscosity as a function of the overlap parameter C[η]. The variation of the exponent s obtained from the power law η~γ˙^−s for both flow and dynamic results is discussed in terms of Graessley’s analysis. In the semi-dilute regime with entanglements, a dynamic master curve is obtained as a function of DNA concentration (C_DNA > 2.0 mg/mL) and temperature (10 °C < T < 40 °C).

Monitoring structural changes in intrinsically disordered proteins using QCM-D: application to the bacterial cell division protein ZipA

Characterization of structural changes in an intrinsically disordered protein attached on a QCM-D, with a sensitivity of 1.8 nm or better.

Asynchronous Magnetic Bead Rotation (AMBR) Microviscometer for Label-Free DNA Analysis

We have developed a label-free viscosity-based DNA detection system, using paramagnetic beads as an asynchronous magnetic bead rotation (AMBR) microviscometer. We have demonstrated experimentally that the bead rotation period is linearly proportional to the viscosity of a DNA solution surrounding the paramagnetic bead, as expected theoretically. Simple optical measurement of asynchronous microbead motion determines solution viscosity precisely in microscale volumes, thus allowing an estimate of DNA concentration or average fragment length. The response of the AMBR microviscometer yields reproducible measurement of DNA solutions, enzymatic digestion reactions, and PCR systems at template concentrations across a 5000-fold range. The results demonstrate the feasibility of viscosity-based DNA detection using AMBR in microscale aqueous volumes.

A micro-liter viscosity and density sensor for the rheological characterization of DNA solutions in the kilo-hertz range

When measuring the properties of fluids from biological sources, sample volumes in the micro-liter range are often desired as higher volumes may not be available or are very expensive. Miniaturized viscosity and density sensors based on a vibrating cantilever fulfill this requirement. In this paper, the possibility of measuring viscosity and density of DNA solutions at the same time using such a sensor is shown. The sensor requires a sample volume of 10 μl. By doing a titration of a solution containing 110 bp long strands of DNA in the diluted, Newtonian regime, the intrinsic viscosity can be determined to be 0.047 ml mg(-1) using the cantilever sensor. The cantilever is also tested with solutions of 10 kbp long strands with concentrations in the semi-dilute, non-Newtonian regime. The comparably small change in resonance frequency and damping observed using these solutions at 12.5 kHz is attributed to shear thinning, which is expected when extrapolating results from other groups.